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91.
Gene-based tests of association can increase the power of a genome-wide association study by aggregating multiple independent effects across a gene or locus into a single stronger signal. Recent gene-based tests have distinct approaches to selecting which variants to aggregate within a locus, modeling the effects of linkage disequilibrium, representing fractional allele counts from imputation, and managing permutation tests for p-values. Implementing these tests in a single, efficient framework has great practical value. Fast ASsociation Tests (Fast) addresses this need by implementing leading gene-based association tests together with conventional SNP-based univariate tests and providing a consolidated, easily interpreted report. Fast scales readily to genome-wide SNP data with millions of SNPs and tens of thousands of individuals, provides implementations that are orders of magnitude faster than original literature reports, and provides a unified framework for performing several gene based association tests concurrently and efficiently on the same data. Availability: https://bitbucket.org/baderlab/fast/downloads/FAST.tar.gz, with documentation at https://bitbucket.org/baderlab/fast/wiki/Home 相似文献
92.
Pritam Mohanty Shashikanta Behera Swasti S. Swain Durga P. Barik Soumendra K. Naik 《Physiology and Molecular Biology of Plants》2013,19(4):605-610
An optimized protocol was developed for in vitro plant regeneration of a medicinally important herb Hedychium coronarium J. Koenig using sprouted buds of rhizomes. The rhizomes with sprouted bud were inoculated on Murashige and Skoog (Physiol Plant 15:473–497, 1962) medium (MS) supplemented with either N6-benzyladenine (BA) alone (1.0–4.0 mg L−1) or in combination with 0.5 mg L−1 naphthalene acetic acid (NAA). Of these combinations, MS supplemented with a combination of 2.0 mg L−1 BA and 0.5 mg L−1 NAA was most effective. In this medium, best shoots (3.6) and roots (4.0) regeneration was observed simultaneously with an average shoot and root length of 4.7 cm and 4.2 cm respectively. Regeneration of shoots and roots in the same medium at the same time (One step shoot and root regeneration) reduced the time for production of in vitro plantlets and eliminates the media cost of rooting. Cent-percent (100 %) success in plant establishment was observed in both gradual acclimatization process as well as when plants were directly transferred to outdoor in clay pots containing a mixture of garden soil and sand (2:1) without any sequential acclimatization stage. 相似文献
93.
Indian Journal of Microbiology - Bioremediation is a process wherein the decontamination strategies are designed so that a site could achieve the environmental abiotic and biotic parameters close... 相似文献
94.
95.
Shoot apices of Pinus roxburghii Sarg were cultured on Murashige and Skoog’s medium (MS) supplemented with cytokinins [6-benzyladenine (BA), kinetin and N-benzyl-9-(2-tetrahydropyranyl)
adenine (BPA)] alone and in combination with auxin, α-napthaleneacetic acid (NAA). Of the three cytokinins tested at varying
concentrations, medium supplemented with 10 μM BA was found optimal in respect of explant responsiveness (97.22 %) and average
number of buds induced per explant (7.42). The concentration of cytokinins in the induction medium had a profound effect on
rate of elongation of induced buds on MS basal medium containing 0.5 % activated charcoal. Further, shoots induced on lower
concentrations of BA increased up to 2.4 times in length in 4 weeks. Decapitation of the explant enhanced the rate of axillary
bud elongation. Proliferating shoot cultures were established by sub-culturing the axillary shoots on MS supplemented with
10 μM BA. Shoots 2–3 cm in length were suitable for culturing as more buds were induced on them compared to longer or shorter
shoots. Root primordia were induced on 70.83 % shoots when transferred to 1/2 MS medium supplemented with 5.0 μM NAA. Elongation
of root primordia (60 %) was achieved in liquid 1/2 MS basal medium. The plantlets were successfully transferred to soil after
hardening; the time period from initiation of shoot buds to transplantation being 20–22 weeks. 相似文献
96.
Bacterial identification on the basis of the highly conserved 16S rRNA (rrs) gene is limited by its presence in multiple copies and a very high level of similarity among them. The need is to look for other genes with unique characteristics to be used as biomarkers. Fifty-one sequenced genomes belonging to 10 different Yersinia species were used for searching genes common to all the genomes. Out of 304 common genes, 34 genes of sizes varying from 0.11 to 4.42 kb, were selected and subjected to in silico digestion with 10 different Restriction endonucleases (RE) (4–6 base cutters). Yersinia species have 6–7 copies of rrs per genome, which are difficult to distinguish by multiple sequence alignments or their RE digestion patterns. However, certain unique combinations of other common gene sequences—carB, fadJ, gluM, gltX, ileS, malE, nusA, ribD, and rlmL and their RE digestion patterns can be used as markers for identifying 21 strains belonging to 10 Yersinia species: Y. aldovae, Y. enterocolitica, Y. frederiksenii, Y. intermedia, Y. kristensenii, Y. pestis, Y. pseudotuberculosis, Y. rohdei, Y. ruckeri, and Y. similis. This approach can be applied for rapid diagnostic applications.
Electronic supplementary material
The online version of this article (doi:10.1007/s12088-015-0552-6) contains supplementary material, which is available to authorized users. 相似文献97.
Saurabh Sudha Dhiman Gaurav Garg Jitender Sharma Vipin C. Kalia Yun Chan Kang Jung-Kul Lee 《PloS one》2014,9(7)
In order to reduce the ecotoxicity of paper mill, four different enzymatic pretreatment strategies were investigated in comparison to conventional chemical based processes. In strategy I, xylanase-aided pretreatment of pulp was carried out, and in strategy II, xylanase and laccase-mediator systems were used sequentially. Moreover, to compare the efficiency of Bacillus stearothermophilus xylanase and Ceriporiopsis subvermispora laccase in the reduction of ecotoxicity and pollution, parallel strategies (III and IV) were implemented using commercial enzymes. Conventional CDEOPD1D2 (CD, Cl2 with ClO2; EOP, H2O2 extraction; D1 and D2, ClO2) and X/XLCDEOPD1D2 (X, xylanase; L, laccase) sequences were employed with non-enzymatic and enzymatic strategies, respectively. Acute toxicity was determined by the extent of inhibition of bioluminescence of Vibrio fischeri with different dilutions of the effluent. Two-fold increase was observed in EC50 values for strategy I compared to the control process. On the other hand, sequential application of commercial enzymes resulted in higher acute toxicity compared to lab enzymes. In comparison to the control process, strategy II was the most efficient and successfully reduced 60.1 and 25.8% of biological oxygen demand (BOD) and color of effluents, respectively. We report for the first time the comparative analysis of the ecotoxicity of industrial effluents. 相似文献
98.
Chanhyung Bae Jeet Kalia Inhye Song JeongHeon Yu Ha Hyung Kim Kenton J. Swartz Jae Il Kim 《PloS one》2012,7(12)
A unique peptide toxin, named double-knot toxin (DkTx), was recently purified from the venom of the tarantula Ornithoctonus huwena and was found to stably activate TRPV1 channels by targeting the outer pore domain. DkTx has been shown to consist of two inhibitory cysteine-knot (ICK) motifs, referred to as K1 and K2, each containing six cysteine residues. Beyond this initial characterization, however, the structural and functional details about DkTx remains elusive in large part due to the lack of a high yielding methodology for the synthesis and folding of this cysteine-rich peptide. Here, we overcome this obstacle by generating pure DkTx in quantities sufficient for structural and functional analyses. Our methodology entails expression of DkTx in E. coli followed by oxidative folding of the isolated linear peptide. Upon screening of various oxidative conditions for optimizing the folding yield of the toxin, we observed that detergents were required for efficient folding of the linear peptide. Our synthetic DkTx co-eluted with the native toxin on HPLC, and irreversibly activated TRPV1 in a manner identical to native DkTx. Interestingly, we find that DkTx has two interconvertible conformations present in a 1∶6 ratio at equilibrium. Kinetic analysis of DkTx folding suggests that the K1 and K2 domains influence each other during the folding process. Moreover, the CD spectra of the toxins shows that the secondary structures of K1 and K2 remains intact even after separating the two knots. These findings provide a starting point for detailed studies on the structural and functional characterization of DkTx and utilization of this toxin as a tool to explore the elusive mechanisms underlying the polymodal gating of TRPV1. 相似文献
99.
In testis, seminiferous epithelium is one of the most productive self-renewing systems in which apoptosis is an important phenomenon. Alteration in the cellular redox status has several detrimental effects on the cells, one of which is increased rate of apoptotic signals disturbing the natural balance. Since apoptotic responses to various therapeutic agents and toxicants follow diverse molecular mechanisms, therefore, the present study was designed to explore apoptosis in testes under the effect of oxidative stress. Tertiary butyl hydroperoxide (tBHP) was used to induce oxidative stress in mice. It was found that ROS production in testes by tBHP resulted in increased apoptosis. The apoptosis was evident from TUNEL staining in Zenker-fixed paraffin-embedded testicular sections of tBHP treated mice testis and DNA fragmentation analysis. Increased mRNA and protein expression of p53 in testis were observed by using RT-PCR and ELISA techniques, respectively. This indicates that p53 expression is linked to ROS generation in mice testes. The functional status of p53 was also assessed by upregulation of cyclin dependent kinase inhibitor, p21. Thus tBHP induced oxidative stress subject testicular cells to apoptosis which seems to involve p53. 相似文献
100.
Molecular biology and pathogenesis of hepatitis E virus 总被引:1,自引:0,他引:1
The hepatitis E virus (HEV) is a small RNA virus and the etiological agent for hepatitis E, a form of acute viral hepatitis.
The virus has a feco-oral transmission cycle and is transmitted through environmental contamination, mainly through drinking
water. Recent studies on the isolation of HEV-like viruses from animal species also suggest zoonotic transfer of the virus.
The absence of small animal models of infection and efficient cell culture systems has precluded virological studies on the
replication cycle and pathogenesis of HEV. A vaccine against HEV has undergone successful clinical testing and diagnostic
tests are available. This review describes HEV epidemiology, clinical presentation, pathogenesis, molecular virology and the
host response to HEV infection. The focus is on published literature in the past decade.
Equal contribution 相似文献